i've had the same experience with a large strongback that i was sure was strong and rigid. every time i lined something up, something else was out of whack - and this did not make any sense - one should be able to get it better and better.

so i pulled everything apart and tried flexing the strongback and noticed it really bent at one location. so i took it all apart and there was an almost total failure across one of the strongback pces. (this was a 6"x3" x 5/8 plywood internal s/b). remade the s/b, and things started working from there.

if you have a good rigid base (s/b) to work from, things will work out.
be patient and find out what the prob is first.

everything starts with a good foundation.